Phylo cookbook

Revision as of 16:01, 25 June 2010

Here are some examples of using Bio.Phylo for some likely tasks. Some of the given functions might be added to Biopython in a later release, but you can use them in your own code with Biopython 1.54.

Consensus methods

TODO:

• Majority-rules consensus

Rooting methods

TODO:

• Root at the midpoint between the two most distant nodes (or "center" of all tips)
• Root with the given outgroup (terminal or nonterminal)

Exporting to other types

Convert to a PyCogent tree

The tree objects used by Biopython and PyCogent are different. Nonetheless, both toolkits support the Newick file format, so interoperability is straightforward at that level:

from Bio import Phylo
import cogent
 
Phylo.write(bptree, 'mytree.nwk', 'newick')  # Biopython tree
ctree = cogent.LoadTree('mytree.nwk')        # PyCogent tree

TODO:

• Convert objects directly, preserving some PhyloXML annotations if possible

Convert to a NumPy array or matrix

TODO:

• Adjacency matrix: cells are True if parent-child relationship exists, otherwise False
• Distance matrix: cells are branch lengths if a branch exists, otherwise Inf or NaN
• Relationship matrix? See Martins and Housworth 2002